BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 031743
(153 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3IZR|V Chain V, Localization Of The Large Subunit Ribosomal Proteins Into
A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
Ribosome
Length = 171
Score = 258 bits (658), Expect = 1e-69, Method: Compositional matrix adjust.
Identities = 124/151 (82%), Positives = 132/151 (87%)
Query: 1 MVKYSKEPDNPTKSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPF 60
MVKYS+E +NPTKS KA G DLRVHFKNTRETA AIRKLPL KAKRYLEDV+AHKQAIPF
Sbjct: 1 MVKYSREANNPTKSSKAMGRDLRVHFKNTRETAFAIRKLPLGKAKRYLEDVIAHKQAIPF 60
Query: 61 TRFCGGVGRTAQAKNRHPNGQGRWPVKSAKFILDLLKNAESNAEVKGLDVDALYISHIQV 120
R+CGGVGRTAQAK+RH NGQGRWP KSA+FILDLLKNAESNAEVKGLDVD LY+SHIQV
Sbjct: 61 RRYCGGVGRTAQAKSRHSNGQGRWPAKSARFILDLLKNAESNAEVKGLDVDTLYVSHIQV 120
Query: 121 NQAQKQRRRTYRAHGRINRMFLVLFHLCLIF 151
NQAQKQRRRTYRAHGRIN H+ LI
Sbjct: 121 NQAQKQRRRTYRAHGRINPYMSSPCHIELIL 151
>pdb|2ZKR|RR Chain r, Structure Of A Mammalian Ribosomal 60s Subunit Within An
80s Complex Obtained By Docking Homology Models Of The
Rna And Proteins Into An 8.7 A Cryo-Em Map
Length = 184
Score = 196 bits (498), Expect = 4e-51, Method: Compositional matrix adjust.
Identities = 97/151 (64%), Positives = 117/151 (77%), Gaps = 1/151 (0%)
Query: 1 MVKYSKEPDNPTKSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPF 60
MV+YS +P+NPTKSCK+RGS+LRVHFKNTRETA AI+ + + KA +YL+DV KQ +PF
Sbjct: 1 MVRYSLDPENPTKSCKSRGSNLRVHFKNTRETAQAIKGMHIRKATKYLKDVTLQKQCVPF 60
Query: 61 TRFCGGVGRTAQAKNRHPNGQGRWPVKSAKFILDLLKNAESNAEVKGLDVDALYISHIQV 120
R+ GGVGR AQAK QGRWP KSA+F+L +LKNAESNAE+KGLDVD+L I HIQV
Sbjct: 61 RRYNGGVGRCAQAKQWGWT-QGRWPKKSAEFLLHMLKNAESNAELKGLDVDSLVIEHIQV 119
Query: 121 NQAQKQRRRTYRAHGRINRMFLVLFHLCLIF 151
N+A K RRRTYRAHGRIN H+ +I
Sbjct: 120 NKAPKMRRRTYRAHGRINPYMSSPCHIEMIL 150
>pdb|2WW9|I Chain I, Cryo-Em Structure Of The Active Yeast Ssh1 Complex Bound
To The Yeast 80s Ribosome
pdb|2WWA|I Chain I, Cryo-Em Structure Of Idle Yeast Ssh1 Complex Bound To The
Yeast 80s Ribosome
pdb|2WWB|I Chain I, Cryo-Em Structure Of The Mammalian Sec61 Complex Bound To
The Actively Translating Wheat Germ 80s Ribosome
pdb|3O58|Q Chain Q, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The First 80s In The Asymmetric Unit.
pdb|3O5H|Q Chain Q, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
Of The Second 80s In The Asymmetric Unit.
pdb|3U5E|P Chain P, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome A
pdb|3U5I|P Chain P, The Structure Of The Eukaryotic Ribosome At 3.0 A
Resolution. This Entry Contains Proteins Of The 60s
Subunit, Ribosome B
pdb|4B6A|P Chain P, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
With Arx1 And Rei1
Length = 184
Score = 177 bits (448), Expect = 3e-45, Method: Compositional matrix adjust.
Identities = 88/150 (58%), Positives = 103/150 (68%), Gaps = 1/150 (0%)
Query: 1 MVKYSKEPDNPTKSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPF 60
M +Y NP KS ARGS LRV FKNTRETA AI LTKA++YLE V+ H++AIPF
Sbjct: 1 MARYGATSTNPAKSASARGSYLRVSFKNTRETAQAINGWELTKAQKYLEQVLDHQRAIPF 60
Query: 61 TRFCGGVGRTAQAKNRHPNGQGRWPVKSAKFILDLLKNAESNAEVKGLDVDALYISHIQV 120
RF +GRTAQ K + RWP KS KF+ LL+NA +NAE KGLD LY+SHIQV
Sbjct: 61 RRFNSSIGRTAQGKE-FGVTKARWPAKSVKFVQGLLQNAAANAEAKGLDATKLYVSHIQV 119
Query: 121 NQAQKQRRRTYRAHGRINRMFLVLFHLCLI 150
NQA KQRRRTYRAHGRIN+ H+ L+
Sbjct: 120 NQAPKQRRRTYRAHGRINKYESSPSHIELV 149
>pdb|3IZS|V Chain V, Localization Of The Large Subunit Ribosomal Proteins Into
A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
Translating 80s Ribosome
Length = 170
Score = 176 bits (447), Expect = 3e-45, Method: Compositional matrix adjust.
Identities = 88/150 (58%), Positives = 103/150 (68%), Gaps = 1/150 (0%)
Query: 1 MVKYSKEPDNPTKSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPF 60
M +Y NP KS ARGS LRV FKNTRETA AI LTKA++YLE V+ H++AIPF
Sbjct: 1 MARYGATSTNPAKSASARGSYLRVSFKNTRETAQAINGWELTKAQKYLEQVLDHQRAIPF 60
Query: 61 TRFCGGVGRTAQAKNRHPNGQGRWPVKSAKFILDLLKNAESNAEVKGLDVDALYISHIQV 120
RF +GRTAQ K + RWP KS KF+ LL+NA +NAE KGLD LY+SHIQV
Sbjct: 61 RRFNSSIGRTAQGKEFGVT-KARWPAKSVKFVQGLLQNAAANAEAKGLDATKLYVSHIQV 119
Query: 121 NQAQKQRRRTYRAHGRINRMFLVLFHLCLI 150
NQA KQRRRTYRAHGRIN+ H+ L+
Sbjct: 120 NQAPKQRRRTYRAHGRINKYESSPSHIELV 149
>pdb|1S1I|N Chain N, Structure Of The Ribosomal 80s-Eef2-Sordarin Complex From
Yeast Obtained By Docking Atomic Models For Rna And
Protein Components Into A 11.7 A Cryo-Em Map. This File,
1s1i, Contains 60s Subunit. The 40s Ribosomal Subunit Is
In File 1s1h
Length = 183
Score = 174 bits (441), Expect = 2e-44, Method: Compositional matrix adjust.
Identities = 87/149 (58%), Positives = 102/149 (68%), Gaps = 1/149 (0%)
Query: 2 VKYSKEPDNPTKSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFT 61
+Y NP KS ARGS LRV FKNTRETA AI LTKA++YLE V+ H++AIPF
Sbjct: 1 ARYGATSTNPAKSASARGSYLRVSFKNTRETAQAINGWELTKAQKYLEQVLDHQRAIPFR 60
Query: 62 RFCGGVGRTAQAKNRHPNGQGRWPVKSAKFILDLLKNAESNAEVKGLDVDALYISHIQVN 121
RF +GRTAQ K + RWP KS KF+ LL+NA +NAE KGLD LY+SHIQVN
Sbjct: 61 RFNSSIGRTAQGKE-FGVTKARWPAKSVKFVQGLLQNAAANAEAKGLDATKLYVSHIQVN 119
Query: 122 QAQKQRRRTYRAHGRINRMFLVLFHLCLI 150
QA KQRRRTYRAHGRIN+ H+ L+
Sbjct: 120 QAPKQRRRTYRAHGRINKYESSPSHIELV 148
>pdb|3JYW|N Chain N, Structure Of The 60s Proteins For Eukaryotic Ribosome
Based On Cryo-Em Map Of Thermomyces Lanuginosus Ribosome
At 8.9a Resolution
Length = 150
Score = 172 bits (437), Expect = 5e-44, Method: Compositional matrix adjust.
Identities = 87/147 (59%), Positives = 101/147 (68%), Gaps = 1/147 (0%)
Query: 4 YSKEPDNPTKSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRF 63
Y NP KS ARGS LRV FKNTRETA AI LTKA++YLE V+ H++AIPF RF
Sbjct: 1 YGATSTNPAKSASARGSYLRVSFKNTRETAQAINGWELTKAQKYLEQVLDHQRAIPFRRF 60
Query: 64 CGGVGRTAQAKNRHPNGQGRWPVKSAKFILDLLKNAESNAEVKGLDVDALYISHIQVNQA 123
+GRTAQ K + RWP KS KF+ LL+NA +NAE KGLD LY+SHIQVNQA
Sbjct: 61 NSSIGRTAQGKEFGVT-KARWPAKSVKFVQGLLQNAAANAEAKGLDATKLYVSHIQVNQA 119
Query: 124 QKQRRRTYRAHGRINRMFLVLFHLCLI 150
KQRRRTYRAHGRIN+ H+ L+
Sbjct: 120 PKQRRRTYRAHGRINKYESSPSHIELV 146
>pdb|4A17|Q Chain Q, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 2.
pdb|4A1A|Q Chain Q, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 3.
pdb|4A1C|Q Chain Q, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 4.
pdb|4A1E|Q Chain Q, T.Thermophila 60s Ribosomal Subunit In Complex With
Initiation Factor 6. This File Contains 5s Rrna, 5.8s
Rrna And Proteins Of Molecule 1
Length = 183
Score = 154 bits (390), Expect = 1e-38, Method: Compositional matrix adjust.
Identities = 83/137 (60%), Positives = 94/137 (68%), Gaps = 5/137 (3%)
Query: 4 YSKEPDNPTKSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRF 63
YS+EP N K+ K SDLRVHFKNT E AI+ L L AKRYL+ V+ K+ IPFTRF
Sbjct: 6 YSREPANQAKAVKTSASDLRVHFKNTYEVVRAIKGLNLENAKRYLKAVIDRKRCIPFTRF 65
Query: 64 CGGVGRTAQAKNRHPNG--QGRWPVKSAKFILDLLKNAESNAEVKGLDVDALYISHIQVN 121
G +GRTAQA H G QGRWPVKS K IL LL N +NA+ K L+ L I H QVN
Sbjct: 66 TGCIGRTAQA---HEFGRTQGRWPVKSVKVILGLLDNLSANAQAKSLNTANLVIQHGQVN 122
Query: 122 QAQKQRRRTYRAHGRIN 138
+AQK RRRTYRAHGRIN
Sbjct: 123 RAQKGRRRTYRAHGRIN 139
>pdb|3ZF7|R Chain R, High-resolution Cryo-electron Microscopy Structure Of The
Trypanosoma Brucei Ribosome
Length = 166
Score = 132 bits (333), Expect = 5e-32, Method: Compositional matrix adjust.
Identities = 72/151 (47%), Positives = 96/151 (63%), Gaps = 1/151 (0%)
Query: 1 MVKYSKEPDNPTKSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPF 60
MV YS++P +K+ KA+ +DLR H+KNT ETA+ I + L KA++ V+A + IPF
Sbjct: 1 MVHYSRKPQVSSKTAKAKIADLRCHYKNTFETANVINGMKLRKAQQLYRQVLAKTRCIPF 60
Query: 61 TRFCGGVGRTAQAKNRHPNGQGRWPVKSAKFILDLLKNAESNAEVKGLDVDALYISHIQV 120
R+ G +G TAQAK +GRWP KS +L LLKNAE+NA KGLD + I H+QV
Sbjct: 61 KRYNGKIGNTAQAKEWG-QTKGRWPRKSVVAMLSLLKNAEANAIEKGLDPGKMVIKHVQV 119
Query: 121 NQAQKQRRRTYRAHGRINRMFLVLFHLCLIF 151
+QA + RRRT+RAHGRI H+ L
Sbjct: 120 DQAPRVRRRTFRAHGRITPYMRSPCHVQLFM 150
>pdb|1S72|R Chain R, Refined Crystal Structure Of The Haloarcula Marismortui
Large Ribosomal Subunit At 2.4 Angstrom Resolution
pdb|1YHQ|R Chain R, Crystal Structure Of Azithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YI2|R Chain R, Crystal Structure Of Erythromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIJ|R Chain R, Crystal Structure Of Telithromycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YIT|R Chain R, Crystal Structure Of Virginiamycin M And S Bound To The
50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJN|R Chain R, Crystal Structure Of Clindamycin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1YJW|R Chain R, Crystal Structure Of Quinupristin Bound To The G2099a
Mutant 50s Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ4|R Chain R, The Structure Of The Transition State Analogue "daa" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ5|R Chain R, The Structure Of The Transition State Analogue "raa" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ6|R Chain R, The Structure Of C-Hpmn And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ7|R Chain R, The Structure Of The Transition State Analogue "dca" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQ8|R Chain R, The Structure Of Ccda-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQ9|R Chain R, The Structure Of Cca-Phe-Cap-Bio And The Antibiotic
Sparsomycin Bound To The Large Ribosomal Subunit Of
Haloarcula Marismortui
pdb|1VQK|R Chain R, The Structure Of Ccda-Phe-Cap-Bio Bound To The A Site Of
The Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQL|R Chain R, The Structure Of The Transition State Analogue "dcsn"
Bound To The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1VQM|R Chain R, The Structure Of The Transition State Analogue "dan" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQN|R Chain R, The Structure Of Cc-hpmn And Cca-phe-cap-bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|1VQO|R Chain R, The Structure Of Ccpmn Bound To The Large Ribosomal
Subunit Haloarcula Marismortui
pdb|1VQP|R Chain R, The Structure Of The Transition State Analogue "rap" Bound
To The Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|2OTJ|R Chain R, 13-Deoxytedanolide Bound To The Large Subunit Of
Haloarcula Marismortui
pdb|2OTL|R Chain R, Girodazole Bound To The Large Subunit Of Haloarcula
Marismortui
pdb|2QA4|R Chain R, A More Complete Structure Of The The L7L12 STALK OF THE
Haloarcula Marismortui 50s Large Ribosomal Subunit
pdb|3CC2|R Chain R, The Refined Crystal Structure Of The Haloarcula
Marismortui Large Ribosomal Subunit At 2.4 Angstrom
Resolution With Rrna Sequence For The 23s Rrna And
Genome-Derived Sequences For R-Proteins
pdb|3CC4|R Chain R, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|3CC7|R Chain R, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2487u
pdb|3CCE|R Chain R, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535a
pdb|3CCJ|R Chain R, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation C2534u
pdb|3CCL|R Chain R, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation U2535c. Density For Anisomycin Is
Visible But Not Included In Model.
pdb|3CCM|R Chain R, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2611u
pdb|3CCQ|R Chain R, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488u
pdb|3CCR|R Chain R, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation A2488c. Density For Anisomycin Is
Visible But Not Included In The Model.
pdb|3CCS|R Chain R, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482a
pdb|3CCU|R Chain R, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2482c
pdb|3CCV|R Chain R, Structure Of Anisomycin Resistant 50s Ribosomal Subunit:
23s Rrna Mutation G2616a
pdb|3CD6|R Chain R, Co-cystal Of Large Ribosomal Subunit Mutant G2616a With
Cc-puromycin
pdb|3CPW|Q Chain Q, The Structure Of The Antibiotic Linezolid Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CMA|R Chain R, The Structure Of Cca And Cca-Phe-Cap-Bio Bound To The
Large Ribosomal Subunit Of Haloarcula Marismortui
pdb|3CME|R Chain R, The Structure Of Ca And Cca-Phe-Cap-Bio Bound To The Large
Ribosomal Subunit Of Haloarcula Marismortui
pdb|2QEX|R Chain R, Negamycin Binds To The Wall Of The Nascent Chain Exit
Tunnel Of The 50s Ribosomal Subunit
pdb|3I55|R Chain R, Co-Crystal Structure Of Mycalamide A Bound To The Large
Ribosomal Subunit
pdb|3I56|R Chain R, Co-Crystal Structure Of Triacetyloleandomcyin Bound To The
Large Ribosomal Subunit
pdb|4ADX|R Chain R, The Cryo-Em Structure Of The Archaeal 50s Ribosomal
Subunit In Complex With Initiation Factor 6
Length = 155
Score = 75.9 bits (185), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 46/137 (33%), Positives = 75/137 (54%), Gaps = 4/137 (2%)
Query: 2 VKYSKEPDNPTKSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFT 61
+ YS E D P + KA + ++ FK+++ A I+ +A YLE V+ Q +PF
Sbjct: 3 ISYSVEAD-PDTTAKAMLRERQMSFKHSKAIAREIKGKTAGEAVDYLEAVIEGDQPVPFK 61
Query: 62 RFCGGVGRTAQAKNRHPNGQGRWPVKSAKFILDLLKNAESNAEVKGLDVDALYISHIQVN 121
+ GVG ++ GR+P K++K LDLL+NA NA+ +G D +A+ I H+ +
Sbjct: 62 QHNSGVGHKSKVDGWD---AGRYPEKASKAFLDLLENAVGNADHQGFDGEAMTIKHVAAH 118
Query: 122 QAQKQRRRTYRAHGRIN 138
+ +Q+ R RA GR +
Sbjct: 119 KVGEQQGRKPRAMGRAS 135
>pdb|3G4S|R Chain R, Co-Crystal Structure Of Tiamulin Bound To The Large
Ribosomal Subunit
pdb|3G6E|R Chain R, Co-Crystal Structure Of Homoharringtonine Bound To The
Large Ribosomal Subunit
pdb|3G71|R Chain R, Co-crystal Structure Of Bruceantin Bound To The Large
Ribosomal Subunit
pdb|3OW2|Q Chain Q, Crystal Structure Of Enhanced Macrolide Bound To 50s
Ribosomal Subunit
Length = 150
Score = 75.5 bits (184), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 46/137 (33%), Positives = 75/137 (54%), Gaps = 4/137 (2%)
Query: 2 VKYSKEPDNPTKSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFT 61
+ YS E D P + KA + ++ FK+++ A I+ +A YLE V+ Q +PF
Sbjct: 2 ISYSVEAD-PDTTAKAMLRERQMSFKHSKAIAREIKGKTAGEAVDYLEAVIEGDQPVPFK 60
Query: 62 RFCGGVGRTAQAKNRHPNGQGRWPVKSAKFILDLLKNAESNAEVKGLDVDALYISHIQVN 121
+ GVG ++ GR+P K++K LDLL+NA NA+ +G D +A+ I H+ +
Sbjct: 61 QHNSGVGHKSKVDGWD---AGRYPEKASKAFLDLLENAVGNADHQGFDGEAMTIKHVAAH 117
Query: 122 QAQKQRRRTYRAHGRIN 138
+ +Q+ R RA GR +
Sbjct: 118 KVGEQQGRKPRAMGRAS 134
>pdb|1FFK|O Chain O, Crystal Structure Of The Large Ribosomal Subunit From
Haloarcula Marismortui At 2.4 Angstrom Resolution
pdb|1JJ2|Q Chain Q, Fully Refined Crystal Structure Of The Haloarcula
Marismortui Large Ribosomal Subunit At 2.4 Angstrom
Resolution
pdb|1KQS|Q Chain Q, The Haloarcula Marismortui 50s Complexed With A
Pretranslocational Intermediate In Protein Synthesis
pdb|1K8A|S Chain S, Co-Crystal Structure Of Carbomycin A Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1K9M|S Chain S, Co-Crystal Structure Of Tylosin Bound To The 50s Ribosomal
Subunit Of Haloarcula Marismortui
pdb|1KD1|S Chain S, Co-crystal Structure Of Spiramycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M1K|S Chain S, Co-Crystal Structure Of Azithromycin Bound To The 50s
Ribosomal Subunit Of Haloarcula Marismortui
pdb|1M90|S Chain S, Co-Crystal Structure Of Cca-Phe-Caproic Acid-Biotin And
Sparsomycin Bound To The 50s Ribosomal Subunit
pdb|1K73|S Chain S, Co-Crystal Structure Of Anisomycin Bound To The 50s
Ribosomal Subunit
pdb|1KC8|S Chain S, Co-Crystal Structure Of Blasticidin S Bound To The 50s
Ribosomal Subunit
pdb|1N8R|S Chain S, Structure Of Large Ribosomal Subunit In Complex With
Virginiamycin M
pdb|1NJI|S Chain S, Structure Of Chloramphenicol Bound To The 50s Ribosomal
Subunit
pdb|1Q7Y|S Chain S, Crystal Structure Of Ccdap-puromycin Bound At The Peptidyl
Transferase Center Of The 50s Ribosomal Subunit
pdb|1Q81|S Chain S, Crystal Structure Of Minihelix With 3' Puromycin Bound To
A- Site Of The 50s Ribosomal Subunit.
pdb|1Q82|S Chain S, Crystal Structure Of Cc-Puromycin Bound To The A-Site Of
The 50s Ribosomal Subunit
pdb|1Q86|S Chain S, Crystal Structure Of Cca-Phe-Cap-Biotin Bound
Simultaneously At Half Occupancy To Both The A-Site And
P- Site Of The The 50s Ribosomal Subunit.
pdb|1QVF|Q Chain Q, Structure Of A Deacylated Trna Minihelix Bound To The E
Site Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1QVG|Q Chain Q, Structure Of Cca Oligonucleotide Bound To The Trna Binding
Sites Of The Large Ribosomal Subunit Of Haloarcula
Marismortui
pdb|1W2B|Q Chain Q, Trigger Factor Ribosome Binding Domain In Complex With 50s
pdb|3CXC|Q Chain Q, The Structure Of An Enhanced Oxazolidinone Inhibitor Bound
To The 50s Ribosomal Subunit Of H. Marismortui
Length = 154
Score = 75.5 bits (184), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 46/137 (33%), Positives = 75/137 (54%), Gaps = 4/137 (2%)
Query: 2 VKYSKEPDNPTKSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFT 61
+ YS E D P + KA + ++ FK+++ A I+ +A YLE V+ Q +PF
Sbjct: 2 ISYSVEAD-PDTTAKAMLRERQMSFKHSKAIAREIKGKTAGEAVDYLEAVIEGDQPVPFK 60
Query: 62 RFCGGVGRTAQAKNRHPNGQGRWPVKSAKFILDLLKNAESNAEVKGLDVDALYISHIQVN 121
+ GVG ++ GR+P K++K LDLL+NA NA+ +G D +A+ I H+ +
Sbjct: 61 QHNSGVGHKSKVDGWD---AGRYPEKASKAFLDLLENAVGNADHQGFDGEAMTIKHVAAH 117
Query: 122 QAQKQRRRTYRAHGRIN 138
+ +Q+ R RA GR +
Sbjct: 118 KVGEQQGRKPRAMGRAS 134
>pdb|3J21|S Chain S, Promiscuous Behavior Of Proteins In Archaeal Ribosomes
Revealed By Cryo-em: Implications For Evolution Of
Eukaryotic Ribosomes (50s Ribosomal Proteins)
Length = 155
Score = 73.2 bits (178), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 50/133 (37%), Positives = 68/133 (51%), Gaps = 4/133 (3%)
Query: 4 YSKEPDNPTKSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFTRF 63
YS + +P + +A DLR+ K E +R + L A RYL+DV+A K+ +P R+
Sbjct: 7 YSFQNFDPKRMARASARDLRISPKLAVEVCRELRGMMLNDALRYLDDVIALKRPVPLKRY 66
Query: 64 CGGVGRTAQAKNRHPNGQGRWPVKSAKFILDLLKNAESNAEVKGLDVDALYISHIQVNQA 123
G K G GR+PVK AK I +L N ++NA KGLD D L I HI ++
Sbjct: 67 NDSQGH----KPGKGFGPGRYPVKVAKAIKKVLLNVKNNAVQKGLDPDKLKIIHIAAHKG 122
Query: 124 QKQRRRTYRAHGR 136
R RA GR
Sbjct: 123 PVLRGWYPRAFGR 135
>pdb|1YJ9|R Chain R, Crystal Structure Of The Mutant 50s Ribosomal Subunit Of
Haloarcula Marismortui Containing A Three Residue
Deletion In L22
Length = 152
Score = 70.1 bits (170), Expect = 4e-13, Method: Compositional matrix adjust.
Identities = 47/135 (34%), Positives = 71/135 (52%), Gaps = 7/135 (5%)
Query: 2 VKYSKEPDNPTKSCKARGSDLRVHFKNTRETAHAIRKLPLTKAKRYLEDVMAHKQAIPFT 61
+ YS E D P + KA + ++ FK+++ A I+ +A YLE V+ Q +PF
Sbjct: 3 ISYSVEAD-PDTTAKAMLRERQMSFKHSKAIAREIKGKTAGEAVDYLEAVIEGDQPVPFK 61
Query: 62 RFCGGVGRTAQAKNRHPNGQGRWPVKSAKFILDLLKNAESNAEVKGLDVDALYISHIQVN 121
+ GVG ++ GR+P K++K LDLL+NA NA+ +G D +A+ I H+
Sbjct: 62 QHNSGVGHKSKVDGWD---AGRYPEKASKAFLDLLENAVGNADHQGFDGEAMTIKHV--- 115
Query: 122 QAQKQRRRTYRAHGR 136
A K R RA GR
Sbjct: 116 AAHKVGERKPRAMGR 130
>pdb|1CBR|A Chain A, Crystal Structure Of Cellular Retinoic-Acid-Binding
Proteins I And Ii In Complex With All-Trans-Retinoic
Acid And A Synthetic Retinoid
pdb|1CBR|B Chain B, Crystal Structure Of Cellular Retinoic-Acid-Binding
Proteins I And Ii In Complex With All-Trans-Retinoic
Acid And A Synthetic Retinoid
pdb|2CBR|A Chain A, Cellular Retinoic Acid Binding Protein I In Complex With A
Retinobenzoic Acid (Am80)
pdb|1CBI|A Chain A, Apo-Cellular Retinoic Acid Binding Protein I
pdb|1CBI|B Chain B, Apo-Cellular Retinoic Acid Binding Protein I
Length = 136
Score = 28.5 bits (62), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 26/49 (53%)
Query: 78 PNGQGRWPVKSAKFILDLLKNAESNAEVKGLDVDALYISHIQVNQAQKQ 126
PN G W ++S++ +LLK NA ++ + V A H+++ Q Q
Sbjct: 1 PNFAGTWKMRSSENFDELLKALGVNAMLRKVAVAAASKPHVEIRQDGDQ 49
>pdb|3BE5|A Chain A, Crystal Structure Of Fite (Crystal Form 1), A Group Iii
Periplasmic Siderophore Binding Protein
pdb|3BE5|B Chain B, Crystal Structure Of Fite (Crystal Form 1), A Group Iii
Periplasmic Siderophore Binding Protein
pdb|3BE5|C Chain C, Crystal Structure Of Fite (Crystal Form 1), A Group Iii
Periplasmic Siderophore Binding Protein
pdb|3BE5|D Chain D, Crystal Structure Of Fite (Crystal Form 1), A Group Iii
Periplasmic Siderophore Binding Protein
pdb|3BE6|A Chain A, Crystal Structure Of Fite (Crystal Form 2), A Group Iii
Periplasmic Siderophore Binding Protein
pdb|3BE6|B Chain B, Crystal Structure Of Fite (Crystal Form 2), A Group Iii
Periplasmic Siderophore Binding Protein
pdb|3BE6|C Chain C, Crystal Structure Of Fite (Crystal Form 2), A Group Iii
Periplasmic Siderophore Binding Protein
pdb|3BE6|D Chain D, Crystal Structure Of Fite (Crystal Form 2), A Group Iii
Periplasmic Siderophore Binding Protein
Length = 297
Score = 25.8 bits (55), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 24/48 (50%)
Query: 92 ILDLLKNAESNAEVKGLDVDALYISHIQVNQAQKQRRRTYRAHGRINR 139
IL+ A+ NA LD + +S IQ NQ + +Y + GR+ R
Sbjct: 142 ILERRYQAQINALKATLDSQKITVSVIQANQGKINVXHSYHSLGRVLR 189
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.324 0.136 0.413
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,212,614
Number of Sequences: 62578
Number of extensions: 151070
Number of successful extensions: 525
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 498
Number of HSP's gapped (non-prelim): 16
length of query: 153
length of database: 14,973,337
effective HSP length: 90
effective length of query: 63
effective length of database: 9,341,317
effective search space: 588502971
effective search space used: 588502971
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 47 (22.7 bits)